copied from Nucleic Acids Research, 2005, Vol. 33, Database issue (link directs to table of contents with many original papers on the below mentioned databases)
return to Database resources and links

No.b Database_name____ Full_name_and/or_description______________________ URL 4. Structure Databases 4.1. Small molecules 646 ChEBI Chemical entities of biological interest http://www.ebi.ac.uk/chebi/ 261 CSD Cambridge structural database: crystal structure information for organic and metal-organic compounds http://www.ccdc.cam.ac.uk/prods/csd/csd.html 265 HIC-Up Hetero-compound Information Centre—Uppsala http://xray.bmc.uu.se/hicup 402 AANT Amino acid–nucleotide interaction database http://aant.icmb.utexas.edu/ 111 Klotho Collection and categorization of biological compounds http://www.biocheminfo.org/klotho 113 LIGAND Chemical compounds and reactions in biological pathways http://www.genome.ad.jp/ligand/ 615 PDB-Ligand 3D structures of small molecules bound to proteins and nucleic acids http://www.idrtech.com/PDB-Ligand/ 735 PubChem Structures and biological activities of small organic molecules http://pubchem.ncbi.nlm.nih.gov/ 4.2. Carbohydrates 429 CCSD Complex carbohydrate structure database (CarbBank) http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm 652 CSS Carbohydrate structure suite: carbohydrate 3D structures derived from the PDB http://www.dkfz.de/spec/css/ 486 Glycan Carbohydrate database, part of the KEGG system http://glycan.genome.ad.jp/ 292 GlycoSuiteDB N- and O-linked glycan structures and biological sources http://www.glycosuite.com/ 535 Monosaccharide Browser Space-filling Fischer projections of monosaccharides http://www.jonmaber.demon.co.uk/monosaccharide 300 SWEET-DB Annotated carbohydrate structure and substance information http://www.dkfz-heidelberg.de/spec2/sweetdb/ 4.3. Nucleic acid structure 272 NDB Nucleic acid-containing structures http://ndbserver.rutgers.edu/ 273 NTDB Thermodynamic data for nucleic acids http://ntdb.chem.cuhk.edu.hk/ 387 RNABase RNA-containing structures from PDB and NDB http://www.rnabase.org/ 283 SCOR Structural classification of RNA: RNA motifs by structure, function and tertiary interactions http://scor.lbl.gov/ 4.4. Protein structure 413 ArchDB Automated classification of protein loop structures http://gurion.imim.es/archdb 255 ASTRAL Sequences of domains of known structure, selected subsets and sequence–structure correspondences http://astral.stanford.edu/ 288 BAliBASE A database for comparison of multiple sequence alignments http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html 257 BioMagResBank NMR spectroscopic data for proteins and nucleic acids http://www.bmrb.wisc.edu/ 384 CADB Conformational angles in proteins database http://cluster.physics.iisc.ernet.in/cadb/ 258 CATH Protein domain structures database http://www.biochem.ucl.ac.uk/bsm/cath_new 259 CE 3D protein structure alignments http://cl.sdsc.edu/ce.html 260 CKAAPs DB Structurally similar proteins with dissimilar sequences http://ckaap.sdsc.edu/ 442 Dali Protein fold classification using the Dali search engine http://www.bioinfo.biocenter.helsinki.fi:8080/dali/ 385 Decoys ‘R’ Us Computer-generated protein conformations http://dd.stanford.edu/ 447 DisProt Database of Protein Disorder: proteins that lack fixed 3D structure in their native states http://divac.ist.temple.edu/disprot 448 DomIns Domain insertions in known protein structures http://stash.mrc-lmb.cam.ac.uk/DomIns 264 DSDBASE Native and modeled disulfide bonds in proteins http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html 386 DSMM Database of simulated molecular motions http://projects.villa-bosch.de/dbase/dsmm/ 452 eF-site Electrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active sites http://ef-site.protein.osaka-u.ac.jp/eF-site 674 GenDiS Genomic distribution of protein structural superfamilies http://caps.ncbs.res.in/gendis/home.html 472 Gene3D Precalculated structural assignments for whole genomes http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/ 489 GTD Genomic threading database: structural annotations of complete proteomes http://bioinf.cs.ucl.ac.uk/GTD 322 GTOP Protein fold predictions from genome sequences http://spock.genes.nig.ac.jp/~genome/ 360 Het-PDB Navi Hetero-atoms in protein structures http://daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html 498 HOMSTRAD Homologous structure alignment database: curated structure-based alignments for protein families http://www-cryst.bioc.cam.ac.uk/homstrad 267 IMB Jena Image Library Visualization and analysis of 3D biopolymer structures http://www.imb-jena.de/IMAGE.html 502 IMGT/3Dstructure-DB Sequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins http://imgt3d.igh.cnrs.fr/ 268 ISSD Integrated sequence–structure database http://www.protein.bio.msu.su/issd 269 LPFC Library of protein family core structures http://www-smi.stanford.edu/projects/helix/LPFC 270 MMDB NCBI's database of 3D structures, part of NCBI Entrez http://www.ncbi.nlm.nih.gov/Structure 456 E-MSD EBI's macromolecular structure database http://www.ebi.ac.uk/msd 331 ModBase Annotated comparative protein structure models http://alto.compbio.ucsf.edu/modbase-cgi/index.cgi 262 MolMovDB Database of macromolecular movements: descriptions of protein and macromolecular motions, including movies http://bioinfo.mbb.yale.edu/MolMovDB/ 274 PALI Phylogeny and alignment of homologous protein structures http://pauling.mbu.iisc.ernet.in/~pali 275 PASS2 Structural motifs of protein superfamilies http://ncbs.res.in/~faculty/mini/campass/pass.html 557 PepConfDB A database of peptide conformations http://www.peptidome.org/products/list.htm 276 PDB Protein structure databank: all publicly available 3D structures of proteins and nucleic acids http://www.rcsb.org/pdb 277 PDB-REPRDB Representative protein chains, based on PDB entries http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl 278 PDBsum Summaries and analyses of PDB structures http://www.biochem.ucl.ac.uk/bsm/pdbsum 619 PDB_TM Transmembrane proteins with known 3D structure http://www.enzim.hu/PDB_TM/ 719 Protein Folding Database Experimental data on protein folding http://pfd.med.monash.edu.au 282 SCOP Structural classification of proteins http://scop.mrc-lmb.cam.ac.uk/scop 284 Sloop Classification of protein loops http://www-cryst.bioc.cam.ac.uk/~sloop/ 583 Structure Superposition Database Pairwise superposition of TIM-barrel structures http://ssd.rbvi.ucsf.edu/ 585 SWISS-MODEL Repository Database of annotated 3D protein structure models http://swissmodel.expasy.org/repository 285 SUPERFAMILY Assignments of proteins to structural superfamilies http://supfam.org/ 584 SURFACE Surface residues and functions annotated, compared and evaluated: a database of protein surface patches http://cbm.bio.uniroma2.it/surface 764 TargetDB Target data from worldwide structural genomics projects http://targetdb.pdb.org/ 401 3D-GENOMICS Structural annotations for complete proteomes http://www.sbg.bio.ic.ac.uk/3dgenomics 310 TOPS Topology of protein structures database http://www.tops.leeds.ac.uk

^a Each database is shown in the list only once, often in a category that was arbitrarily chosen among two or three appropriate ones. In the online version of this list at the NAR website (http://nar.oupjournals.org/), a database can be listed under two categories.

^b Accession number of the database in the online list; can be used to view the database summary, e.g. http://www3.oup.co.uk/nar/database/summary/1 shows the summary for DDBJ.